lib/CXGN/Chado/Stock.pm

   1 =head1 NAME
   2
   3 CXGN::Chado::Stock - a second-level DBIC Bio::Chado::Schema::Stock::Stock object
   4
   5 Version:1.0
   6
   7 =head1 DESCRIPTION
   8
   9 Created to work with  CXGN::Page::Form::AjaxFormPage
  10 for eliminating the need to refactor the  AjaxFormPage and Editable  to work with DBIC objects.
  11 Functions such as 'get_obsolete' , 'store' , and 'exists_in_database' are required , and do not use standard DBIC syntax.
  12
  13 =head1 AUTHOR
  14
  15 Naama Menda <nm249@cornell.edu>
  16
  17 =cut
  18
  19 package CXGN::Chado::Stock ;
  20 use strict;
  21 use warnings;
  22 use Carp;
  23 use Bio::Chado::Schema;
  24
  25 use base qw / CXGN::DB::Object / ;
  26
  27 =head2 new
  28
  29   Usage: my $stock = CXGN::Chado::Stock->new($schema, $stock_id);
  30   Desc:
  31   Ret: a CXGN::Chado::Stock object
  32   Args: a $schema a schema object,
  33         $stock_id, if omitted, an empty stock object is created.
  34   Side_Effects: accesses the database, check if exists the database columns that this object use. die if the id is not an integer.
  35
  36 =cut
  37
  38 sub new {
  39     my $class = shift;
  40     my $schema = shift;
  41     my $id = shift;
  42
  43      ### First, bless the class to create the object and set the schema into the object.
  44     #my $self = $class->SUPER::new($schema);
  45     my $self = bless {}, $class;
  46     $self->set_schema($schema);
  47     my $stock;
  48     if (defined $id) {
  49         $stock = $self->get_resultset('Stock::Stock')->find({ stock_id => $id });
  50     } else {
  51         ### Create an empty resultset object;
  52         $stock = $self->get_resultset('Stock::Stock')->new( {} );
  53     }
  54     ###It's important to set the object row for using the accesor in other class functions
  55     $self->set_object_row($stock);
  56     return $self;
  57 }
  58
  59
  60
  61 =head2 store
  62
  63  Usage: $self->store
  64  Desc:  store a new stock
  65  Ret:   a database id
  66  Args:  none
  67  Side Effects: checks if the stock exists in the database, and if does, will attempt to update
  68  Example:
  69
  70 =cut
  71
  72 sub store {
  73     my $self=shift;
  74     my $id = $self->get_stock_id();
  75     my $schema=$self->get_schema();
  76     #no stock id . Check first if the name  exists in te database
  77     if (!$id) {
  78         my $exists= $self->exists_in_database();
  79         if (!$exists) {
  80             my $new_row = $self->get_object_row();
  81             $new_row->insert();
  82
  83             $id=$new_row->stock_id();
  84         }else {
  85             my $existing_stock=$self->get_resultset('Stock::Stock')->find($exists);
  86             #don't update here if stock already exist. User should call from the code exist_in_database
  87             #and instantiate a new stock object with the database id
  88             #updating here is not a good idea, since it might not be what the user intended to do
  89             #and it can mess up the database.
  90         }
  91     }else { # id exists
  92         $self->get_object_row()->update();
  93     }
  94     return $id
  95 }
  96
  97 ########################
  98
  99
 100 =head2 exists_in_database
 101
 102  Usage: $self->exists_in_database()
 103  Desc:  check if the uniquename exists in the stock table
 104  Ret:
 105  Args:
 106  Side Effects:
 107  Example:
 108
 109 =cut
 110
 111 sub exists_in_database {
 112     my $self=shift;
 113     my $stock_id = $self->get_stock_id();
 114     my $uniquename = $self->get_uniquename || '' ;
 115     my ($s) = $self->get_resultset('Stock::Stock')->search(
 116         {
 117             uniquename  => { 'ilike' => $uniquename },
 118         });
 119     #loading new stock - $stock_id is undef
 120     if (defined($s) && !$stock_id ) {  return $s->stock_id ; }
 121
 122     #updating an existing stock
 123     elsif ($stock_id && defined($s) ) {
 124         if ( ($s->stock_id == $stock_id) ) {
 125             return 0;
 126             #trying to update the uniquename
 127         } elsif ( $s->stock_id != $stock_id ) {
 128             return " Can't update an existing stock $stock_id uniquename:$uniquename.";
 129             # if the new name we're trying to update/insert does not exist in the stock table..
 130         } elsif ($stock_id && !$s->stock_id) {
 131             return 0;
 132         }
 133     }
 134     return undef;
 135 }
 136
 137 =head2 get_organism
 138
 139  Usage: $self->get_organism
 140  Desc:  find the organism object of this stock
 141  Ret:   L<Bio::Chado::Schema::Organism::Organism> object
 142  Args:  none
 143  Side Effects: none
 144  Example:
 145
 146 =cut
 147
 148 sub get_organism {
 149     my $self = shift;
 150     if (my $bcs_stock = $self->get_object_row) {
 151         return $bcs_stock->organism;
 152     }
 153     return undef;
 154 }
 155
 156 =head2 get_type
 157
 158  Usage: $self->get_type
 159  Desc:  find the cvterm type of this stock
 160  Ret:   L<Bio::Chado::Schema::Cv::Cvterm> object
 161  Args:   none
 162  Side Effects: none
 163  Example:
 164
 165 =cut
 166
 167 sub get_type {
 168     my $self = shift;
 169
 170     if (my $bcs_stock = $self->get_object_row ) {
 171         return  $bcs_stock->type;
 172     }
 173     return undef;
 174
 175 }
 176
 177
 178
 179 sub get_object_row {
 180     my $self = shift;
 181     return $self->{object_row};
 182 }
 183
 184 sub set_object_row {
 185   my $self = shift;
 186   $self->{object_row} = shift;
 187 }
 188
 189 =head2 get_resultset
 190
 191  Usage: $self->get_resultset(ModuleName::TableName)
 192  Desc:  Get a ResultSet object for source_name
 193  Ret:   a ResultSet object
 194  Args:  a source name
 195  Side Effects: none
 196  Example:
 197
 198 =cut
 199
 200 sub get_resultset {
 201     my $self=shift;
 202     my $source = shift;
 203     return $self->get_schema()->resultset("$source");
 204 }
 205
 206 =head2 accessors get_schema, set_schema
 207
 208  Usage:
 209  Desc:
 210  Property
 211  Side Effects:
 212  Example:
 213
 214 =cut
 215
 216 sub get_schema {
 217   my $self = shift;
 218   return $self->{schema};
 219 }
 220
 221 sub set_schema {
 222   my $self = shift;
 223   $self->{schema} = shift;
 224 }
 225
 226
 227 ###mapping accessors to DBIC
 228
 229 =head2 accessors get_name, set_name
 230
 231  Usage:
 232  Desc:
 233  Property
 234  Side Effects:
 235  Example:
 236
 237 =cut
 238
 239 sub get_name {
 240     my $self = shift;
 241     return $self->get_object_row()->get_column("name");
 242 }
 243
 244 sub set_name {
 245     my $self = shift;
 246     $self->get_object_row()->set_column(name => shift);
 247 }
 248
 249 =head2 accessors get_uniquename, set_uniquename
 250
 251  Usage:
 252  Desc:
 253  Property
 254  Side Effects:
 255  Example:
 256
 257 =cut
 258
 259 sub get_uniquename {
 260     my $self = shift;
 261     return $self->get_object_row()->get_column("uniquename");
 262 }
 263
 264 sub set_uniquename {
 265     my $self = shift;
 266     $self->get_object_row()->set_column(uniquename => shift);
 267 }
 268
 269 =head2 accessors get_organism_id, set_organism_id
 270
 271  Usage:
 272  Desc:
 273  Property
 274  Side Effects:
 275  Example:
 276
 277 =cut
 278
 279 sub get_organism_id {
 280     my $self = shift;
 281     if (my $bcs_stock =  $self->get_object_row ) {
 282         return $bcs_stock->get_column("organism_id");
 283     }
 284     return undef;
 285 }
 286
 287 sub set_organism_id {
 288     my $self = shift;
 289     $self->get_object_row()->set_column(organism_id => shift);
 290 }
 291
 292 =head2 accessors get_type_id, set_type_id
 293
 294  Usage:
 295  Desc:
 296  Property
 297  Side Effects:
 298  Example:
 299
 300 =cut
 301
 302 sub get_type_id {
 303     my $self = shift;
 304     if (my $bcs_stock = $self->get_object_row ) {
 305         return $bcs_stock->get_column("type_id");
 306     }
 307 }
 308
 309 sub set_type_id {
 310     my $self = shift;
 311     $self->get_object_row()->set_column(type_id => shift);
 312 }
 313
 314 =head2 accessors get_description, set_description
 315
 316  Usage:
 317  Desc:
 318  Property
 319  Side Effects:
 320  Example:
 321
 322 =cut
 323
 324 sub get_description {
 325     my $self = shift;
 326     return $self->get_object_row()->get_column("description");
 327 }
 328
 329 sub set_description {
 330     my $self = shift;
 331     $self->get_object_row()->set_column(description => shift);
 332 }
 333
 334 =head2 accessors get_stock_id, set_stock_id
 335
 336  Usage:
 337  Desc:
 338  Property
 339  Side Effects:
 340  Example:
 341
 342 =cut
 343
 344 sub get_stock_id {
 345     my $self = shift;
 346     if ( my $bcs_stock = $self->get_object_row ) {
 347         return $bcs_stock->get_column("stock_id");
 348     }
 349     return undef;
 350 }
 351
 352 sub set_stock_id {
 353     my $self = shift;
 354     $self->get_object_row()->set_column(stock_id => shift);
 355 }
 356
 357 =head2 accessors get_is_obsolete, set_is_obsolete
 358
 359  Usage:
 360  Desc:
 361  Property
 362  Side Effects:
 363  Example:
 364
 365 =cut
 366
 367 sub get_is_obsolete {
 368     my $self = shift;
 369     my $stock = $self->get_object_row();
 370     return $stock->get_column("is_obsolete") if $stock;
 371 }
 372
 373 sub set_is_obsolete {
 374     my $self = shift;
 375     $self->get_object_row()->set_column(is_obsolete => shift);
 376 }
 377
 378 =head2 function get_image_ids
 379
 380   Synopsis:     my @images = $self->get_image_ids()
 381   Arguments:    none
 382   Returns:      a list of image ids
 383   Side effects: none
 384   Description:  a method for fetching all images associated with a stock
 385
 386 =cut
 387
 388 sub get_image_ids {
 389     my $self = shift;
 390     my $ids = $self->get_schema->storage->dbh->selectcol_arrayref
 391         ( "SELECT value FROM stockprop JOIN cvterm on cvterm.cvterm_id = stockprop.type_id WHERE stock_id=? AND cvterm.name = 'sgn image_id' ",
 392           undef,
 393           $self->get_stock_id
 394         );
 395     return @$ids;
 396 }
 397
 398 ##########
 399 1;########
 400 ##########